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Primers for amplifying bisulfite converted template DNA were designed using MethPrimer software accessible at http://www.urogene.org/methprimer/ (Li and Dahiya, 2002).
In addition, we ruled out unintentional overestimation of cytosine methylation due to an eventual inefficient bisulphite conversion by using primers that were specifically designed to amplify the converted template and were incapable of annealing to the natural template.
In addition, we ruled out a possible unintentional overestimation of cytosine methylation due to an eventual inefficient bisulfite conversion by using primers specifically designed to amplify the converted template but incapable of annealing to the natural sequence.
Nested PCR was performed using an Expand High Fidelity PCR kit (Roche) to amplify fully converted DNA templates.
After bisulfite treatment, DNA was amplified using real-time PCR with oligonucleotide primers complementary to a region of the MYOD1 promoter that did not contain any CpG dinucleotides but did contain non-CpG cytosines to ascertain the amount of converted input templates in each sample.
Inefficient hybridization of the probes to the converted TpA template resulted in the lack of probe extension, and thus very low residual fluorescence signals, both signalMeth and signalUnmeth (see data in Fig. 3a lower panel).
The prototype software for converting COSMIC templates into openEHR archetypes based on the semantic mappings presented above was integrated into the COSMIC template authoring environment.
It is also possible to launch the tool in a batch mode and convert all templates into archetypes at once.
A live software demonstration of converting COSMIC templates to archetypes was successfully performed at the Archetype Workshop at MIE 2008 conference in Gothenburg May 2008 and later at the Danish National SFI Workshop in Copenhagen, November 2008.
Fibreboards made of coir fibres were converted to carbon templates by controlled thermal processing.
All techniques were converted into electronic templates concentrating on domain elements.
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